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Search results for: site-directed mutagenesis
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Modification of quaternary structure of Candida albicans GlcN-6-P synthase and its desensitization to inhibition by UDP-GlcNAc by site-directed mutagenesis
PublicationSite-directed mutagenesis of the CaGFA1 gene encoding glucosamine-6-phosphate synthase from Candida albicans was performed. Desensitization of the enzyme to inhibition by UDPGlcNAc was achieved upon T487I and H492F substitutions at the UDP-GlcNAc binding site, exchange of D524, S525 and S527 for Ala at the dimer:dimer interface and construction of the tail-lock array (L434R and L460A) at the C-tail region. The first two sets if...
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Desensitization of glucosamine-6-phosphate synthase to inhibition by UDP-GlcNAc
PublicationGlucosamine-6-phosphate (GlcN-6-P) synthase, known also as L-Glutamine: D-fructose-6-phosphate amidotransferase, catalyzes the first committed step in the pathway leading to the ultimate formation of UDP-GlcNAc. The final product of this pathway is an activated precursor of numerous macromolecules containing amino sugars, including chitin and mannproteins in fungi, peptidoglycan and lipopolysaccharides in bacteria, and glycoproteins...
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A study on the interaction of rhodamine B with methylthioadenosine phosphorylase protein sourced from an Antarctic soil metagenomic library.
PublicationThe presented study examines the phenomenon of the fluorescence under UV light excitation (312 nm) of E. coli cells expressing a novel metagenomic-derived putative methylthioadenosine phosphorylase gene, called rsfp, grown on LB agar supplemented with a fluorescent dye rhodamine B. For this purpose, an rsfp gene was cloned and expressed in an LMG194 E. coli strain using an arabinose promoter. The resulting RSFP protein was purified...
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Conserved motifs of MutL proteins
PublicationtThe MutL protein is best known for its function in DNA mismatch repair (MMR). However, there isevidence to suggest that MutL is not only the linker connecting the functions of MutS and MutH in MMR,but that it also participates in other repair systems, such as Very Short Patch (VSP), Base Excision (BER)and Nucleotide Excision Repair (NER). This study set out to identify the most highly conserved aminoacid sequence motifs in MutL...
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Wpływ ścieków przemysłowych na energochłonność i efektywność procesów technologicznych w komunalnej oczyszczalni ścieków
PublicationW artykule skupiono się na przedstawieniu wpływu jakości i ilości ścieków przemysłowych wprowadzanych do sieci kanalizacyjnej PEWIK GDYNIA Sp. z o. o. na stabilność procesów technologicznych. Określono również wpływ ścieków przemysłowych na energochłonność i efektywność oraz na wzrost kosztów oczyszczania ścieków komunalnych w Grupowej Oczyszczalni Ścieków „Dębogórze” w latach 2012-2015.
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Directed pulse dynamics
PublicationIntroducing a projection method into a one-dimensional model of a pulse propagation in isotropic media, we derive and investigate a system of equation describing dynamics ultrashort pulses of opposite directions ofpropagation and ones with interaction of directed pulses with different polarization.
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Regulated assembly of lipopolysaccharide and sensing of its alterations in Escherichia coli
PublicationThis thesis describes mechanism of the regulation of the transcription of the rpoE gene encoding an essential RNA polymerase subunit in Escherichia coli. The RpoE regulates extracytoplasmic stress response regulon and is required to initiate transcription of genes, whose products are involvedin the folding of periplasmic proteins and synthesis and transport of outer membrane components. The transcriptional regulation of the rpoE...
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Clearing directed subgraphs by mobile agents
PublicationWe study several problems of clearing subgraphs by mobile agents in digraphs. The agents can move only along directed walks of a digraph and, depending on the variant, their initial positions may be pre-specified. In general, for a given subset S of vertices of a digraph D and a positive integer k, the objective is to determine whether there is a subgraph H=(V,A) of D such that (a) S is a subset of V, (b) H is the union of k directed...
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A construction for the hat problem on a directed graph
PublicationA team of n players plays the following game. After a strategy session, each player is randomly fitted with a blue or red hat. Then, without further communication, everybody can try to guess simultaneously his own hat color by looking at the hat colors of the other players. Visibility is defined by a directed graph; that is, vertices correspond to players, and a player can see each player to whom he is connected by an arc. The...
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THE CIRCUS SITE
PublicationThe location of project is a site of over 1,2 ha, situated on the southern fringes of Gdynia formerly used as an area to host a Circus. Here artists were performing for the public, newcomers were meeting the locals, the temporality of the event was enhancing the experience of exchange. Circus used to be the place where people live, work and create art. Currently the site stays empty but surely not for long. Its potential, attractive...
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Synchronous black hole search in directed graphs
PublicationThe paper considers a team of robots which has to explore a graph G, where some nodes can be harmful. Robots are initially located at the so-called home base node. The dangerous nodes are the so-called black hole nodes, and once a robot enters in one of them, it is destroyed. The goal is to find a strategy in order to explore G in such a way that minimum number of robots is wasted. The exploration ends if there is at least one...
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Projekt Site-Specific / Nanotechnologia
e-Learning CoursesZadanie projektowe odnosi się do działań artystycznych i projektowych z obszaru Site-Specific (temat nanotechnologia ) w przestrzeni miejskiej oraz we wnętrzu. W zadaniu powinna być uwzględniona specyfika przestrzenna Budynku Centrum Nanotechnologii. Należy zaprojektować i zrealizować obiekt lub zespół obiektów w skali 1:1 zintegrowanych z przestrzenią hallu budynku nanotechnologii, względnie jego przestrzeni wejściowej.
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MUTAGENESIS
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Directed percolation effects emerging from superadditivity of quantum networks
PublicationEntanglement-induced nonadditivity of classical communication capacity in networks consisting of quantum channels is considered. Communication lattices consisting of butterfly-type entanglement-breaking channels augmented, with some probability, by identity channels are analyzed. The capacity superadditivity in the network is manifested in directed correlated bond percolation which we consider in two flavors: simply directed and...
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Digitalization of Building Site Management in the Construction Industry
PublicationWith Industry 4.0, a digital transformation has started in the construction industry. However, 4.0 technologies have difficulties in the integration of digital systems due to the diversity and complexity of the processes in the construction industry. Multidisciplinary work in architectural projects and the need for high productivity require digital renovation planning in the construction industry. The application of the technologies...
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A space-efficient algorithm for computing the minimum cycle mean in a directed graph
PublicationAn algorithm is introduced for computing the minimum cycle mean in a strongly connected directed graph with n vertices and m arcs that requires O(n) working space. This is a considerable improvement for sparse graphs in comparison to the classical algorithms that require O(n^2) working space. The time complexity of the algorithm is still O(nm). An implementation in C++ is made publicly available at http://www.pawelpilarczyk.com/cymealg/.
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INTEGRATION OF THE MOBILE PLATFORMS BASED ON SOCIAL NETWORK SERVICE DIRECTED AT USERS LOCALIZATION
PublicationThis paper presents an architecture overview and some aspects of implementation of the social network service directed at users localization. It shows how web services can be used as a tool for integrating different mobile platforms with a web application. The main focus is set on communication between system elements and related problems.
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Projekt SITE-SPECIFIC
e-Learning CoursesW zadaniu projektowym musi być uwzględniona specyfika przestrzenna i historyczna Kampusu Politechniki Gdański. Należy zaprojektować i zrealizować obiekt lub zespół obiektów w skali 1:1 w zintegrowanych z przestrzenią kampusu. Materiałem roboczym w postawionym zadaniu będą trzy stalowe łożyska mostu, każdy o wadze 11 ton.
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On Directed Lattice Paths With Vertical Steps
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Directed laplacian kernels for link analysis
PublicationPrzedstawiono zastosowanie algorytmów opartych o funkcje jądra do problemu analizy linków i cytowań. Zaproponowano nowe funkcje jądra zbudowane na operatorze Laplace'a dla grafów skierowanych. Odzwierciedlają one powiązanie pomiędzy węzłami grafu jako funkcję długości łączących je ścieżek oraz istotności odwiedzanych po drodze węzłów. Eksperymenty z nowymi funkcjami jądra przeprowadzono na zbiorze cytowań pobranych z publikacji...
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A collection of directed graphs for the minimum cycle mean weight computation
Open Research DataThis dataset contains definitions of the 16 directed graphs with weighted edges that were described in the following paper: Paweł Pilarczyk, A space-efficient algorithm for computing the minimum cycle mean in a directed graph, Journal of Mathematics and Computer Science, 20 (2020), no. 4, 349--355, DOI: 10.22436/jmcs.020.04.08, URL: http://dx.doi.org/10.22436/jmcs.020.04.08 These...
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Computer-Aided Saturation Mutagenesis of Arabidopsis thaliana Ent-Copalyl Diphosphate Synthase
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A comparative analysis of methods and tools for low impact development (LID) site selection
PublicationThe site selection for Low Impact Development (LID) practices is a significant process. It affects the effectiveness of LID in controlling stormwater surface runoff, volume, flow rate, and infiltration. This research paper presents a comprehensive review of various methods used for LID site selection. It starts by introducing different methods and tools. Three main methods: index-based methods, GIS-based multi-criteria decision...
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Directed electromagnetic pulse dynamics: projecting operators method
PublicationIn this article, we consider a one-dimensional model of electromagnetic pulse propagation in isotropic media, takinginto account a nonlinearity of the third order. We introduce a method for Maxwell's equation transformation on thebasis of a complete set of projecting operators. The operators correspond to wave dispersion branches including thedirection of propagation. As the simplest result of applying the method, we derive a system...
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Easy and hard instances of arc ranking in directed graphs
PublicationArtykuł dotyczy uporządkowanego kolorowania łuków grafów skierowanych. Problem polega na takim przyporządkowaniu liczb łukom digrafu, aby każda skierowana ścieżka łącząca dwa łuki o tej samej liczbie (kolorze) zawierała łuk o kolorze wyższym. Praca podaje liniowy optymalny algorytm dla pewnego szczególnego przypadku, oraz zawiera dowód, iż problem ten jest obliczeniowo trudny dla 3-dzielnych acyklicznych digrafów i stałej liczby...
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Wisłoujście Fortress, site 12
PublicationThis introductory article provides a synopsis of the range of archaeological work carried out at Wisłoujście Fortress in Gdańsk in 2013 and 2014. An outline is given of the circumstances in which this work was undertaken, the fieldwork methodology used and the technical problems encountered during excavation.
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A tool for integrating Web Site services over User Interface
PublicationCompanies and organizations are building information systems by integrating previously independent applications, together with new developments. This integration process has to deal with existing applications, which can only be used through their specific interfaces, and often cannot be modified. Integration of web applications running remotely and controlled by separate organizations becomes even more complicated, as their user...
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TERATOGENESIS CARCINOGENESIS AND MUTAGENESIS
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ENVIRONMENTAL AND MOLECULAR MUTAGENESIS
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Projekt Site-Specific / Termometr Fahrenheita i Peryskop (Polemoskop) Heweliusza
e-Learning CoursesTematami zadania projektowego będzie twórcza interpretacja termometru Fahrenheita lub peryskopu (polemoskopu) Heweliusza. Zadanie odnosi się do działań artystycznych i projektowych z obszaru Site-Specific. W związku z tym w realizowanych projektach powinien być uwzględniony charakter przestrzeni dziedzińca przed Gmachem Głównym PG. Należy zaprojektować i zrealizować model obiektu w skali 1:1 zintegrowany z w/w wymienioną przestrzenią....
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The site at the cape Zidine in Lopar in the context of coastal residential and commercial complexes of Rab Island
PublicationSince 2013, the “Archaeological topography of the island of Rab” project has approached the island’s archaeology holistically and interdisciplinary, tackling all periods and archaeological evidence present on the island. Nevertheless, mostly due to a large amount of new data, a significant segment of research is devoted to Roman residential and production complexes, located either in the island’s fields or along the coast. Thus,...
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Synchronization helps robots to detect black holes in directed graphs
PublicationPraca zawiera nowe wyniki dla problemu poszukiwania czarnej dziury w grafie skierowanym przez zbiór agentów. Czarna dziura jest węzłem niszczącym wszystkich wchodzącej do niej agentów. Pokazano, że w przypadku, gdy stopień wejściowy czarnej dziury wynosi D, do przeszukania grafu skierowanego w modelu synchronicznym wystarcza O(D 2^D) agentów. Wartość ta jest bliska znanemu z literatury oszacowaniu dolnemu Omega (2^D). W pracy pokazano...
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Site-to-site distance distribution in flexible molecules: theoretical evaluation of the donor and/or acceptor fluorescence decay function
PublicationPrzedstawiono wyrażenie teoretyczne opisujące zależność funkcji zaniku fluorescencji od rozkładu odległości P(r) pomiędzy donorami i akceptorami w giętkich molekułach dwuchromoforowych. Wyrażenie uwzględnia wiekoeksponencjalny zanik izolowanych donorów i akceptorów, a także możliwość niekompletnego oznakowania molekuł akceptorami. Przyjęto, że względne zmiany odległości donorów i akceptorów w czasie życia fluorescencji donora mogą...
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Photogrammetric and computerized report on site model in feasibility study of navigability channel on vistula spit
PublicationIn the report the authors present a course of geodesic and geo-computerized works upon realization of feasibility study of navigability channel on Vistula Spit. A procedure of acquiring verification and modeling of data for requirements of a numeric model of a bottom and site has been presented with construction of original software for 3D visualization of the Vistula Spit area. The activities described in the report can be...
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Effect of Ion and Binding Site on the Conformation of Chosen Glycosaminoglycans at the Albumin Surface
PublicationAlbumin is one of the major components of synovial fluid. Due to its negative surface charge, it plays an essential role in many physiological processes, including the ability to form molecular complexes. In addition, glycosaminoglycans such as hyaluronic acid and chondroitin sulfate are crucial components of synovial fluid involved in the boundary lubrication regime. This study presents the influence of Na+, Mg2+ and Ca2+ ions...
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Adaptive resolution simulation of liquid para-hydrogen: testing the robustness of the quantum-classical adaptive coupling
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Ultrashort Opposite Directed Pulses Dynamics with Kerr Effect and Polarization Account
PublicationWe present the application of projection operator methods to solving the problem of the propagation and interaction of short optical pulses of different polarizations and directions in a nonlinear dispersive medium. We restrict ourselves by the caseof one-dimensional theory, taking into account material dispersion and Kerr nonlinearity. The construction of operators is delivered in two variants: for the Cauchy problem and for the...
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Electrochemically directed biofunctionalization of a lossy-mode resonance optical fiber sensor
PublicationIn this work, we present a direct electrochemical biofunctionalization of an indium-tin-oxide-coated lossy-mode resonance optical fiber sensor. The functionalization using a biotin derivative was performed by cyclic voltammetry in a 10 mM biotin hydrazide solution. All stages of the experiment were simultaneously verified with optical and electrochemical techniques. Performed measurements indicate the presence of a poly-biotin...
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Syntheses of N-Substituted Thymine Thioacetamides. A Novel Approach to Site Selective Acylation of Diaminoalkanes
PublicationA new series of N-substituted thiocarbamoyl derivs. contg. histamine, tryptamine, and other moieties having at least one amino group attached to an aliph. chain has been synthesized from (1-thyminyl)thioacetamide in good isolated yields (69-86%). N-[2-(4-Imidazolyl)ethyl](1-thyminyl)thioacetamide was hydrolyzed to its amide on prolonged heating in water. Ammonium sulfide (20-22% soln. in water) has found interesting new applications...
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A cryptic ribosome binding site, false signals in reporter systems and avoidance of protein translation chaos
PublicationThe expression of reporter gene may be induced by activation of cryptic signalling sequences, as we found while constructing the mutS-lacZ fusion gene. We cloned the Escherichia coli lacZ gene encoding beta-galactosidase into a plasmid vector carrying the Thermus thermophilus mutS gene. The clones expected to produce beta-galactosidase as the C-terminal fusion were selected for the complementation of beta-galactosidase activity...
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Discovery of the anticancer drug vinblastine from the endophytic Alternaria alternata and yield improvement by gamma irradiation mutagenesis
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Imidazolium silanethiolates relevant to the active site of cysteineproteases. A cooperative effect in a chain of NH(+)...S(-) hydrogenbonds
PublicationThree imidazolium silanethiolates relevant to the active site of cysteine proteases have been synthesized and investigated by X-ray diffraction, IR spectroscopy and computational methods. As indicated by crystallographic and FT-IR data in the solid state, the transfer of proton from thiol to imidazole takes place and a thiolato-imidazolium ion pair is formed. The FT-IR spectra of crystalline imidazolium silanethiolates exhibit...
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Site-selective magnetic order of neptunium inNp2Ni17
PublicationWe present the results obtained by superconducting quantum interference device (SQUID) magnetometry, specific heat, and Mossbauer spectroscopy measurements carried out on Np2Ni17 polycrystalline samples. We show that long-range magnetic order, with a moment mu((2b)) similar to 2.25 mu(B), occurs below T-N = 17.5 K on the Np (2b) sites. A nontrivial situation is observed in that the other Np sites (2d) do not take part to the order...
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The profit as in-company evaluation of the construction site effectiveness
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Formation of bubbles from a single nucleation site.
PublicationPrzedstawiono wyniki systematycznych badań eksperymentalnych wrzenia wody destylowanej i metanolu z pojedynczego, sztucznego centrum nukleacji. Jako centra nukleacji służyły otwory wywiercone na czołowej powierzchni miedzianego pręta. Średnice otworów wynosiły: 0.25 mm, 0.60 mm oraz 1.0 mm. Do pomiaru częstotliwości odrywania się pęcherzyków zastosowano układ laser diodowy-fotodioda. Sygnał z fotodiody był rejestrowany za...
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A Highly Selective Biosensor Based on Peptide Directly Derived from the HarmOBP7 Aldehyde Binding Site
PublicationThis paper presents the results of research on determining the optimal length of a peptide chain to eectively bind octanal molecules. Peptides that map the aldehyde binding site in HarmOBP7 were immobilized on piezoelectric transducers. Based on computational studies, four Odorant Binding Protein-derived Peptides (OBPPs) with dierent sequences were selected. Molecular modelling results of ligand docking with selected peptides were...
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Active Site Architecture and Reaction Mechanism Determination of Cold Adapted beta-D-galactosidase from Arthrobacter sp. 32cB
PublicationArthbetaDG is a dimeric, cold-adapted beta-D-galactosidase that exhibits high hydrolytic and transglycosylation activity. A series of crystal structures of its wild form, as well as its ArthbetaDG_E441Q mutein complexes with ligands were obtained in order to describe the mode of its action. The ArthbetaDG_E441Q mutein is an inactive form of the enzyme designed to enable observation of enzyme interaction with its substrate. The...
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Phage-Directed Synthesis of Photoluminescent Zinc Oxide Nanoparticles under Benign Conditions
PublicationBiological systems, especially bacteriophages and peptides, are an attractive green alternative to other known methods of nanoparticle synthesis. In this work, for the first time, bacteriophages were employed to synthesize a specific peptide, capable of producing nanoparticles (NPs). Derivatives of M13 bacteriophage exposing a ZnO-binding peptide (TMGA-LGLKWPV) on either pIII or pVIII phage coat protein were constructed and used...
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Intermolecular Hydrogen Bonding Directed by Aryl–Perfluoroaryl π–π Stacking Interactions
PublicationThe crystal structures of five compounds capable of forming self-complementary hydrogen bonds but crystallizing as catemers or creating more complex crystal structures were compared with their complexes prepared by cocrystallization with perfluoroaryl compounds. The results of X-ray diffraction revealed that in all the cases the π–π stacking interactions caused reorganization of hydrogen bonds and induced creation of the expected...
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Praktyka budowlana/Construction on site training 2022/2023
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